@paulcross: I don't understand what you ask. CpG island should be at 200bp long with high percentage of GC and CpG sequence. Your example is not. It can be within one island or not, still I don't see a point of counting them unless you want to compare between different organisms or whatever.

You asked why people search for them in coding strand, when it's not transcribed. Since CpG is a palindrome, it's always on both strands, so you can search whatever one, coding strands are mostly in the databases.

Our country has a serious deficiency in lighthouses. I assume the main reason is that we have no sea.

@paulcross: I don't understand what you ask. CpG island should be at 200bp long with high percentage of GC and CpG sequence. Your example is not. It can be within one island or not, still I don't see a point of counting them unless you want to compare between different organisms or whatever.

You asked why people search for them in coding strand, when it's not transcribed. Since CpG is a palindrome, it's always on both strands, so you can search whatever one, coding strands are mostly in the databases.

Its just a schematic. I dont think I need to type 200 CG twice!

What you said "Since CpG is a palindrome, it's always on both strands" is wrong. CpG island in one strand, doesn't mean it would appear in another strand. One example is that if coding strand are consisted of 200 CGs , there would be 200 GCs in another strand. Since their transcribe direction are the same( no need to explain ) , there would be no CpG island in template strand at all.

Your example would be two, separated by an elipsis. Ones on complementary strands would not be considered separate islands.

Doesn't methylation lead to histone modification and formation of chromatin... inhibiting separation and hence transcription.

Methylation iinterrupted the transcription factors binds to DNA , then lead to mRNA treanscription decrease. That‘s why we focused on the TFBS methylation status in promoter region, in methylation study.

@paulcross: I'm sorry, but you should refresh your DNA basics.If you have CG on one strand 5'->3', you have GC on the other strand, but 3'->5', that means CG 5'->3'. And that's the same on both strands.

Methylation is on both strands too, since it takes place in the cytosine of CpG site. After replication of DNA, the single stranded methylation marks are quickly recognised and methylated on the daughter strand, which leads to preservation of the methylation pattern through division.

Our country has a serious deficiency in lighthouses. I assume the main reason is that we have no sea.

@paulcross: I'm sorry, but you should refresh your DNA basics.If you have CG on one strand 5'->3', you have GC on the other strand, but 3'->5', that means CG 5'->3'. And that's the same on both strands.

Methylation is on both strands too, since it takes place in the cytosine of CpG site. After replication of DNA, the single stranded methylation marks are quickly recognised and methylated on the daughter strand, which leads to preservation of the methylation pattern through division.

This is your SUMO1 mRNA sequence (same as coding sequence).If you search in page for your "GCGGAAGTG" from your first line, you will find it.

Now select Show reverse complement from the right Customize view menu. This should be your template strand. Try to find there your "CGCCTTCAC" from your second line. You will not. Because that's a 3'->5' direction what you have.You will only find it's reverse orientation "CACTTCCGC" there. Because all sequences are read 5'->3'.

That's the reality of your sequence. If the coding strand separates the polymerase will create new strand also in the 5'->3' direction, so it will actually move on the template strand in the 3'->5' direction. This is because polymerase can add nucleotides to existing 3' end only and the strands have to be anti-parallel.

This is your SUMO1 mRNA sequence (same as coding sequence).If you search in page for your "GCGGAAGTG" from your first line, you will find it.

Now select Show reverse complement from the right Customize view menu. This should be your template strand. Try to find there your "CGCCTTCAC" from your second line. You will not. Because that's a 3'->5' direction what you have.You will only find it's reverse orientation "CACTTCCGC" there. Because all sequences are read 5'->3'.

That's the reality of your sequence. If the coding strand separates the polymerase will create new strand also in the 5'->3' direction, so it will actually move on the template strand in the 3'->5' direction. This is because polymerase can add nucleotides to existing 3' end only and the strands have to be anti-parallel.